rem stringlengths 0 477k | add stringlengths 0 313k | context stringlengths 6 599k |
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}); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER)); p.add(abortButton); add(p, BorderLayout.SOUTH); | } }; abortAction.setEnabled(true); font = new Font("Courier New", Font.PLAIN, 12 ); | public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))... |
output = new JTextArea(25, 80); | output = new JTextArea(25, 120); | public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))... |
Runnable buttonEnabler = new Runnable() { public void run() { waitForProcessCompletion(); SwingUtilities.invokeLater(new Runnable() { public void run() { abortAction.setEnabled(false); } }); } }; new Thread(buttonEnabler).start(); | public EngineExecPanel(String header, Process pr) { super(new BorderLayout()); proc = pr; abortButton = new JButton("Abort"); abortButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { proc.destroy(); } }); JPanel p = new JPanel(new FlowLayout(FlowLayout.CENTER))... | |
proc.destroy(); | proc.destroy(); if ( output != null && output.isEnabled() ) { output.append("Aborted ..."); output.setEnabled(false); | public void actionPerformed(ActionEvent e) { proc.destroy(); } |
} | public void actionPerformed(ActionEvent e) { proc.destroy(); } | |
abortButton.setEnabled(false); | public void waitForProcessCompletion() { try { iss.join(); ess.join(); } catch (InterruptedException ex) { System.out.println("Interrupted while waiting for engine"); } abortButton.setEnabled(false); output.append("Execution halted"); } | |
super("Create Table", | super("New Table", | public CreateTableAction() { super("Create Table", ASUtils.createIcon("NewTable", "Create Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } |
"Create Table", | "New Table", | public CreateTableAction() { super("Create Table", ASUtils.createIcon("NewTable", "Create Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } |
putValue(SHORT_DESCRIPTION, "New Table"); | public CreateTableAction() { super("Create Table", ASUtils.createIcon("NewTable", "Create Table", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } | |
if(paramValues == null) paramValues = new HashMap(); | public Map getParamValues(){ return paramValues; } | |
Font detailsFont = new Font("Default", Font.BOLD, 12); | Font detailsFont = new Font("Default", Font.PLAIN, 14); | public static void main(String[] args) { //set defaults Options.setMissingThreshold(0.5); Options.setSpacingThreshold(0.0); Options.setAssocTest(ASSOC_NONE); Options.setHaplotypeDisplayThreshold(1); Options.setMaxDistance(500); Options.setLDColorScheme(STD_SCHEME); ... |
Font detailsFont = new Font("Default", Font.BOLD, 12); | Font detailsFont = new Font("Default", Font.PLAIN, 14); | public void finished() { if(uc != null) { if(uc.isNewVersionAvailable()) { //theres an update available so lets pop some crap up final JLayeredPane jlp = window.getLayeredPane(); fi... |
try { connection.close(); } catch (IOException e) { logger.log(Level.WARNING, "Error while closing connection. error: " + e.getMessage()); } | closeConnection(); | private void connectionClosed(){ try { this.unregisterInternal(); } catch (Exception e) { logger.severe("Error unregistering for monitoring. error=" + e.getMessage()); } /* close the connection */ try { connection.close(); ... |
logger.severe("Error registering for monitoring. error=" + e.getMessage()); new EstablishConnection().start(); | logger.log(Level.SEVERE, "Error registering alert: " + alertName, e); closeConnection(); | private void connectionOpen(){ try { /* start monitoring */ registerInternal(); logger.info("Registered for alert: " + alertName + ", application: " + sourceConfig.getApplicationConfig().getName()); } catch (Exception e) { ... |
double[][] alleleCounts = new double[filteredHaplos[i][0].getGeno().length][9]; for (int j = 0; j < alleleCounts.length; j++){ for (int k = 0; k < alleleCounts[j].length; k++){ alleleCounts[j][k] = 0; } } for (int j = 0; j < filteredHaplos[i].length; j++){ int curHapNum = lookupPos[i][j]; int[] theGeno = filteredHaplo... | public void paintComponent(Graphics graphics) { if (filteredHaplos == null){ super.paintComponent(graphics); return; } Graphics2D g = (Graphics2D) graphics; g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); ... | |
double maj = 0; for (int z = 0; z < alleleCounts[k].length; z++){ if (alleleCounts[k][z] > maj){ majorAllele[k] = z; maj = alleleCounts[k][z]; } } | majorAllele[k] = Chromosome.getFilteredMarker(markerNums[k]).getMajor(); | public void paintComponent(Graphics graphics) { if (filteredHaplos == null){ super.paintComponent(graphics); return; } Graphics2D g = (Graphics2D) graphics; g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); ... |
ODMGXAWrapper txw = new ODMGXAWrapper(); | log.debug( "Creating instance " + imgFile.getAbsolutePath() ); ODMGXAWrapper txw = new ODMGXAWrapper(); | public static ImageInstance create ( VolumeBase vol, File imgFile ) { ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInstance i = new ImageInstance(); i.volume = vol; i.volumeId = vol.getName(); i.imageFile = imgFile; i.fileSize = imgFile.length(); i.mtime = imgFile.lastModified(); i.fnam... |
Iterator readers = ImageIO.getImageReadersByFormatName("jpg"); ImageReader reader = (ImageReader)readers.next(); | String fname = imageFile.getName(); int lastDotPos = fname.lastIndexOf( "." ); if ( lastDotPos <= 0 || lastDotPos >= fname.length()-1 ) { throw new IOException( "Cannot determine file type extension of " + imageFile.getAbsolutePath() ); } String suffix = fname.substring( lastDotPos+1 ); Iterator readers = ImageIO.getIm... | protected void readImageFile() throws IOException { // Find the JPEG image reader // TODO: THis shoud decode also other readers from fname Iterator readers = ImageIO.getImageReadersByFormatName("jpg"); ImageReader reader = (ImageReader)readers.next(); ImageInputStream iis = null; try { iis = Image... |
new TextMethods().saveHapsToText(orderHaps(haplos, textData), textData.getMultiDprime(), OutputFile); | textData.saveHapsToText(orderHaps(haplos, textData), textData.getMultiDprime(), OutputFile); | private void processFile(String fileName,boolean fileType,String infoFileName){ try { int outputType; long maxDistance; HaploData textData; File OutputFile; File inputFile; inputFile = new File(fileName); if(!inputFile.exists()){ ... |
Arrays.sort(theBlock); | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo... | |
if (Chromosome.getFilteredMarker(selectedMarkers[currentClass]).getMajor() == genos[indexIntoBlock]){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getFilteredMarker(preFiltBlock[q]).getMajor())); | if (Chromosome.getFilteredMarker(selectedMarkers[currentClass]).getMAF() > 0.4){ for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); int theGeno = thisChrom.getFilteredGenotype(selectedMarkers[currentCl... | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo... |
hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getFilteredMarker(preFiltBlock[q]).getMinor())); | if (Chromosome.getFilteredMarker(selectedMarkers[currentClass]).getMajor() == genos[indexIntoBlock]){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getFilteredMarker(preFiltBlock[q]).getMajor())); }else{ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getFilteredMarker(preFiltBlock... | Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blo... |
HaplotypeAssociationNode curHap = (HaplotypeAssociationNode) ham.getChild(curBlock,i); | HaplotypeAssociationNode curHap = (HaplotypeAssociationNode) ham.getChild(curBlock,j); | void export(int tabNum, int format, int start, int stop){ fc.setSelectedFile(new File("")); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION){ File outfile = fc.getSelectedFile(); if (format == PNG_MODE || format == COMPRESSED_PNG_MODE){ BufferedImage ima... |
theBlocks.add(thisBlock); | if (thisBlock.length > 1){ theBlocks.add(thisBlock); } | public void stateChanged(ChangeEvent e) { int tabNum = tabs.getSelectedIndex(); if (tabNum == VIEW_D_NUM || tabNum == VIEW_HAP_NUM){ exportMenuItems[0].setEnabled(true); exportMenuItems[1].setEnabled(true); }else if (tabNum == VIEW_TDT_NUM || tabNum... |
chroms.add(new Chromosome(ped, indiv, genos, false, infile.getName())); | chroms.add(new Chromosome(ped, indiv, genos, infile.getName())); | void prepareHapsInput(File infile) throws IOException, HaploViewException{ //this method is called to suck in data from a file (its only argument) //of genotypes and sets up the Chromosome objects. String currentLine; Vector chroms = new Vector(); byte[] genos = new byte[0]; ... |
r.repaint(); | protected void doCreateRelationship() { try { Relationship r = new Relationship(pp, pkTable, fkTable); pp.add(r); } catch (ArchitectException ex) { logger.error("Couldn't create relationship", ex); JOptionPane.showMessageDialog(pp, "Couldn't create relationship: "+ex.getMessage()); } } | |
int high = V_BORDER+2 + count*BOX_SIZE/2; | int high = 2*V_BORDER + count*BOX_SIZE/2; | public Dimension getPreferredSize() { int count = dPrimeTable.length; int high = V_BORDER+2 + count*BOX_SIZE/2; if (markersLoaded){ high += TICK_BOTTOM + widestMarkerName + TEXT_NUMBER_GAP; } return new Dimension(H_BORDER+2 + BOX_SIZE*(count-1), high); } |
return new Dimension(H_BORDER+2 + BOX_SIZE*(count-1), high); | return new Dimension(2*H_BORDER + BOX_SIZE*(count-1), high); | public Dimension getPreferredSize() { int count = dPrimeTable.length; int high = V_BORDER+2 + count*BOX_SIZE/2; if (markersLoaded){ high += TICK_BOTTOM + widestMarkerName + TEXT_NUMBER_GAP; } return new Dimension(H_BORDER+2 + BOX_SIZE*(count-1), high); } |
gComponent2.translate((size.width - pref.width) / 2, (size.height - pref.height) / 2); | if (!(markersLoaded)){ gComponent2.translate((size.width - pref.width) / 2, (size.height - pref.height) / 2); } else { gComponent2.translate((size.width - pref.width) / 2, 0); } | public void paintComponent(Graphics gComponent){ Dimension size = getSize(); Dimension pref = getPreferredSize(); if (!(alreadyPainted)){ buffIm = new BufferedImage(pref.width, pref.height, BufferedImage.TYPE_3BYTE_BGR); Graphics g = buffIm.getGraphics(); FontMe... |
return; | logger.debug("SQLRelationship: populate is a no-op"); | public void populate() throws ArchitectException { return; } |
checkSystem(); | void run() { PhotovaultSettings settings = PhotovaultSettings.getSettings(); Collection databases = settings.getDatabases(); if ( databases.size() == 0 ) { DbSettingsDlg dlg = new DbSettingsDlg( null, true ); if ( dlg.showDialog() != dlg.APPROVE_OPTION ) { S... | |
fail( getBodyText(), "evaluating test: "+ test ); | fail( getBodyText(), "evaluating test: "+ test.getExpressionText() ); | public void doTag(XMLOutput output) throws Exception { if (test == null && xpath == null) { throw new MissingAttributeException( "test" ); } if (test != null) { if (! test.evaluateAsBoolean(context)) { fail( getBodyText(), "evaluating test: "+ test ); ... |
r1.paint((Graphics2D) pp.getGraphics()); r2.paint((Graphics2D) pp.getGraphics()); | public void testNoCrossingLinesEasy() throws ArchitectException { PlayPen pp = layoutAction.getPlayPen(); SQLDatabase ppdb = pp.getDatabase(); SQLTable tables[] = new SQLTable[4]; TablePane tablePanes[] = new TablePane[tables.length]; for (int i = 0; i < tables.length; i++) { tables[i] = new SQLTable(ppdb, ... | |
r1.paint((Graphics2D) pp.getGraphics()); r2.paint((Graphics2D) pp.getGraphics()); | r1.paint(g); r2.paint(g); g.dispose(); | public void testNoCrossingLinesEasy() throws ArchitectException { PlayPen pp = layoutAction.getPlayPen(); SQLDatabase ppdb = pp.getDatabase(); SQLTable tables[] = new SQLTable[4]; TablePane tablePanes[] = new TablePane[tables.length]; for (int i = 0; i < tables.length; i++) { tables[i] = new SQLTable(ppdb, ... |
this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS)); | public TDTPanel(PedFile pf) throws PedFileException{ if (Options.getAssocTest() == ASSOC_TRIO){ result = TDT.calcTrioTDT(pf); }else{ result = TDT.calcCCTDT(pf); } tableColumnNames.add("#"); tableColumnNames.add("Name"); if (Options.getAssocTest() == AS... | |
tempVect.add(currentResult.getTURatio(Options.getAssocTest())); | if(this.countsOrFreqs == SHOW_SINGLE_FREQS) { tempVect.add(currentResult.getFreqs(Options.getAssocTest())); } else if (this.countsOrFreqs == SHOW_SINGLE_COUNTS) { tempVect.add(currentResult.getTURatio(Options.getAssocTest())); } | public void refreshTable(){ this.removeAll(); Vector tableData = new Vector(); int numRes = Chromosome.getSize(); for (int i = 0; i < numRes; i++){ Vector tempVect = new Vector(); TDTResult currentResult = (TDTResult)result.get(Chromosome.realIndex[i]); t... |
if(Options.getAssocTest() == ASSOC_CC) { JRadioButton countsButton = new JRadioButton("Show CC counts"); JRadioButton ratiosButton = new JRadioButton("Show CC frequencies"); ButtonGroup bg = new ButtonGroup(); bg.add(countsButton); bg.add(ratiosButton); countsButton.addActionListener(this); ratiosButton.addActionList... | public void refreshTable(){ this.removeAll(); Vector tableData = new Vector(); int numRes = Chromosome.getSize(); for (int i = 0; i < numRes; i++){ Vector tempVect = new Vector(); TDTResult currentResult = (TDTResult)result.get(Chromosome.realIndex[i]); t... | |
if (fam.getMember(ind.getIndividualID()) != null){ | if (fam.getMembers().containsKey(ind.getIndividualID())){ | public void parseLinkage(Vector pedigrees) throws PedFileException { int colNum = -1; boolean withOptionalColumn = false; int numLines = pedigrees.size(); Individual ind; this.order = new Vector(); for(int k=0; k<numLines; k++){ StringTokenizer tokenizer = new St... |
if (stylesheet instanceof JellyStylesheet) { JellyStylesheet jellyStyle = (JellyStylesheet) stylesheet; jellyStyle.setOutput(output); } | public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if (stylesheet == null) { throw new MissingAttributeException("stylesheet"); } Object source = getSource(); if (log.isDebugEnabled()) { log.debug("About to evaluate stylesheet on source: "... | |
if (info[4].equals("")){ | if (info[3].equals("")){ | public void parsePhasedData(String[] info) throws IOException, PedFileException{ if (info[4].equals("")){ Chromosome.setDataChrom("none"); }else{ Chromosome.setDataChrom("chr" + info[4]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()... |
Chromosome.setDataChrom("chr" + info[4]); | Chromosome.setDataChrom("chr" + info[3]); | public void parsePhasedData(String[] info) throws IOException, PedFileException{ if (info[4].equals("")){ Chromosome.setDataChrom("none"); }else{ Chromosome.setDataChrom("chr" + info[4]); } Chromosome.setDataBuild("ncbi_b35"); Vector sampleData = new Vector()... |
putValue(SHORT_DESCRIPTION, "Delete Selected"); putValue(ACCELERATOR_KEY, KeyStroke.getKeyStroke(KeyEvent.VK_DELETE, 0)); setEnabled(false); | public DeleteSelectedAction() { super("Delete Selected", ASUtils.createJLFIcon("general/Delete", "Delete Selected", ArchitectFrame.getMainInstance().sprefs.getInt(SwingUserSettings.ICON_SIZE, 24))); } | |
if (logger.isDebugEnabled()) { newMenu.addSeparator(); JMenuItem showListeners = new JMenuItem("Show Listeners"); showListeners.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { SQLObject so = (SQLObject) getLastSelectedPathComponent(); if (so != null) { JOptionPane.showMessageDialog... | protected JPopupMenu setupPopupMenu() { JPopupMenu newMenu = new JPopupMenu(); newMenu.add(popupDBCSMenu = new JMenu("Add Connection")); newMenu.addSeparator(); // index 1 JMenuItem popupProperties = new JMenuItem(new DBCSPropertiesAction()); newMenu.add(popupProperties); // index 2 return newMenu; } | |
if (log.isDebugEnabled()) { log.debug( "Firing template body for match: " + match + " and node: " + node ); } | protected Action createAction() { return new Action() { public void run(Node node) throws Exception { xpathSource = node; getBody().run(context, output); } }; } | |
if (log.isDebugEnabled()) { log.debug( "Firing template body for match: " + match + " and node: " + node ); } | public void run(Node node) throws Exception { xpathSource = node; getBody().run(context, output); } | |
if ( log.isDebugEnabled() ) { log.debug( "adding template rule for match: " + match ); } | public void doTag(XMLOutput output) throws Exception { // for use by inner classes this.output = output; StylesheetTag tag = (StylesheetTag) findAncestorWithClass( StylesheetTag.class ); if (tag == null) { throw new JellyException( "This <template> tag must be used ins... | |
URL log4jPropertyURL = Photovault.class.getClassLoader().getResource( "log4j.properties"); | URL log4jPropertyURL = Photovault.class.getClassLoader().getResource( "photovault_log4j.properties"); | public static void main( String [] args ) { URL log4jPropertyURL = Photovault.class.getClassLoader().getResource( "log4j.properties"); PropertyConfigurator.configure( log4jPropertyURL ); Photovault app = new Photovault(); app.run(); } |
public Destination getDestination() { | public Destination getDestination() throws JellyException, JMSException { if (destination == null) { if (subject != null) { destination = findDestination(subject); } } | public Destination getDestination() { return destination; } |
sb.append(text.replace(' ', '_')); | sb.append(toIdentifier(text)); | protected void appendIdentifier(StringBuffer sb, String text) { sb.append(text.replace(' ', '_')); } |
parent.addChild(t); | public static SQLTable getDerivedInstance(SQLTable source, SQLDatabase parent) throws ArchitectException { SQLTable t = new SQLTable(parent); t.columnsPopulated = true; t.relationshipsPopulated = true; t.tableName = source.tableName; t.remarks = source.remarks; t.inherit(source); return t; } | |
String runString = "java -Xmx650m -classpath " + jarfile; | String runString = "java -Xmx10m -classpath " + jarfile; | public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.cl... |
if ((line = besr.readLine()) != null) { errorMsg.append(line); child.destroy(); dead = true; | while ( !dead && (line = besr.readLine()) != null) { if(line.lastIndexOf("Memory") != -1) { errorMsg.append(line); child.destroy(); dead = true; } | public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.cl... |
JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, errorMsg, null, JOptionPane.ERROR_MESSAGE); | Runnable showRip = new Runnable() { public void run() { JFrame jf = new JFrame(); JOptionPane.showMessageDialog(jf, realErrorMsg, null, JOptionPane.ERROR_MESSAGE);} }; SwingUtilities.invokeAndWait(showRip); | public static void main(String[] args) { int exitValue = 0; String dir = System.getProperty("user.dir"); String sep = System.getProperty("file.separator"); String ver = System.getProperty("java.version"); System.out.println(ver); String jarfile = System.getProperty("java.cl... |
assertEquals("We did not generate move events",1,eventCounter.getMoved()); | assertEquals("Even in Compound edits should still generate a move event for each setLocation",2,eventCounter.getMoved()); | public void testMovement() { component.addPlayPenComponentListener( eventCounter); assertEquals("" + "We started out with the wrong number of events", 0,eventCounter.getEvents() ); //component.setMoving(true); //assertEquals("We did not generate a move start event",1,eventCounter.getStarts()); pp.startCompound... |
assertEquals("We did not generate move events",2,eventCounter.getMoved()); | assertEquals("We did not generate move events",3,eventCounter.getMoved()); | public void testMovement() { component.addPlayPenComponentListener( eventCounter); assertEquals("" + "We started out with the wrong number of events", 0,eventCounter.getEvents() ); //component.setMoving(true); //assertEquals("We did not generate a move start event",1,eventCounter.getStarts()); pp.startCompound... |
Widget parent = getParentWidget(); Widget widget = (Widget) createWidget(theClass, parent, style); if (parent != null) { attachWidgets(parent, widget); } | Widget parent = getParentWidget(); | protected Object newInstance( Class theClass, Map attributes, XMLOutput output) throws JellyTagException { int style = getStyle(attributes); // now lets call the constructor with the parent Widget parent = getParentWidget(); Widget widget = (Widget) createWidget(theClass, parent, style); if (parent != null) {... |
return widget; } | Widget widget = (Widget) createWidget(theClass, parent, style); if (parent != null) { attachWidgets(parent, widget); } return widget; } | protected Object newInstance( Class theClass, Map attributes, XMLOutput output) throws JellyTagException { int style = getStyle(attributes); // now lets call the constructor with the parent Widget parent = getParentWidget(); Widget widget = (Widget) createWidget(theClass, parent, style); if (parent != null) {... |
int allele1=0, allele2=0, hom=0, het=0; | int allele1=0, allele2=0, hom=0, het=0, haploid = 0; | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
if(Chromosome.getDataChrom().equalsIgnoreCase("chrx")){ | if(Chromosome.getDataChrom().equals("chrx")){ | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
if(allele1 != allele2) { founderHetCount++; } else{ founderHomCount[allele1]++; } | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... | |
count[allele2]++; | if (!Chromosome.getDataChrom().equals("chrx") || currentInd.getGender() != 1) { if(allele1 != allele2) { founderHetCount++; }else{ founderHomCount[allele1]++; } count[allele2]++; } | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
if(allele1 == allele2) { hom++; } else { het++; | if (!Chromosome.getDataChrom().equals("chrx") || currentInd.getGender() != 1) { if(allele1 == allele2) { hom++; }else { het++; } }else{ haploid++; | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
double genopct = getGenoPercent(het, hom, missing); | double genopct = getGenoPercent(het, hom, haploid, missing); | private MarkerResult checkMarker(int loc)throws PedFileException{ MarkerResult result = new MarkerResult(); Individual currentInd; //int indivgeno=0, int missing=0, founderHetCount=0, mendErrNum=0; int allele1=0, allele2=0, hom=0, het=0; //Hashtable allgenos = new Hashtable... |
private double getGenoPercent(int het, int hom, int missing){ if (het+hom+missing == 0){ | private double getGenoPercent(int het, int hom, int haploid, int missing){ if (het+hom+haploid+missing == 0){ | private double getGenoPercent(int het, int hom, int missing){ if (het+hom+missing == 0){ return 0; }else{ return 100.0*(het+hom)/(het+hom+missing); } } |
return 100.0*(het+hom)/(het+hom+missing); | return 100.0*(het+hom+haploid)/(het+hom+haploid+missing); | private double getGenoPercent(int het, int hom, int missing){ if (het+hom+missing == 0){ return 0; }else{ return 100.0*(het+hom)/(het+hom+missing); } } |
log.info( "Parsing XPath expression: " + attributeValue ); | if ( log.isDebugEnabled() ) { log.debug( "Parsing XPath expression: " + attributeValue ); } | public Expression createExpression( ExpressionFactory factory, String tagName, String attributeName, String attributeValue) throws JellyException { // #### may need to include some namespace URI information in the XPath instance? if (attributeName.equals("select")) ... |
ProjectTag projectTag = (ProjectTag) findAncestorWithClass( ProjectTag.class ); Project project = projectTag.getProject(); | Project project = getProject(); if (project == null) { throw new JellyException("No Project available"); } | public void doTag(final XMLOutput output) throws Exception { AttainTag attainTag = (AttainTag) findAncestorWithClass( AttainTag.class ); Session session = null; if ( attainTag == null ) { session = new JellySession( output ); } else { session = attainTag.get... |
((XMLWriter)contentHandler).flush(); | if( contentHandler instanceof XMLWriter ) { ((XMLWriter)contentHandler).flush(); } | public void flush() throws IOException { ((XMLWriter)contentHandler).flush(); } |
WeblogicApplicationForm appForm = (WeblogicApplicationForm)actionForm; | ApplicationForm appForm = (ApplicationForm)actionForm; | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { WeblogicApplicationForm ap... |
new Integer(appForm.getPort()), | port, | public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { WeblogicApplicationForm ap... |
response.commit(); | public void handle(String pathInContext, String pathParams, HttpRequest request, HttpResponse response) throws HttpException, IOException { Tag handlerTag = (Tag) _tagMap.get(request.getMethod().toLowerCase()); if (null != han... | |
super.setAttribute( name, value.toString() ); | if ( value instanceof Expression ) { super.setAttribute( name, ((Expression) value).evaluateAsValue(context) ); } else { super.setAttribute( name, value.toString() ); } | public void setAttribute(String name, Object value) { if ( value == null ) { // should we send in null? super.setAttribute( name, "" ); } else { super.setAttribute( name, value.toString() ); } } |
ApplicationHeartBeatThread associatedThread = null; for(ApplicationHeartBeatThread thread:threads){ if(thread.getApplicationConfig().equals(appConfig)){ associatedThread = thread; break; } } if(associatedThread == null){ logger.log(Level.WARNING, "Thread not found for application: {0}", appConfig); }else{ threads.remov... | removeApplication(appConfig); addApplication(appConfig); | private void applicationChanged(ApplicationConfig appConfig) { ApplicationHeartBeatThread associatedThread = null; for(ApplicationHeartBeatThread thread:threads){ if(thread.getApplicationConfig().equals(appConfig)){ associatedThread = thread; break; ... |
}else if(event instanceof ApplicationRemovedEvent){ removeApplication(((ApplicationRemovedEvent)event).getApplicationConfig()); | public void start() { for (ApplicationConfig appConfig : ApplicationConfigManager .getAllApplications()) { // only add non-cluster applications if(!appConfig.isCluster()) addApplication(appConfig); } // TODO: perfect dependency to be i... | |
}else if(event instanceof ApplicationRemovedEvent){ removeApplication(((ApplicationRemovedEvent)event).getApplicationConfig()); | public void handleEvent(EventObject event) { if(!(event instanceof ApplicationEvent)){ throw new IllegalArgumentException("event must be of type ApplicationEvent"); } if(event instanceof NewApplicationEvent){ addApplication((... | |
InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + url); Properties properties = new Properties(); try { in = url.openStream(); properties.load(in); for (Iterator iter = properties.entryS... | Properties properties = getJellyProperties(); for (Iterator iter = properties.entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String uri = (String) entry.getKey(); String className = (String) entry.getValue(); String libraryURI = "jelly:" + uri; if ( ! context.isTagLibraryRegister... | protected void configure() { // load the properties file of libraries available InputStream in = null; URL url = getClassLoader().getResource("org/apache/commons/jelly/jelly.properties"); if (url != null) { log.debug("Loading Jelly default tag libraries from: " + ur... |
value = false; if ( test != null ) { | ChooseTag tag = (ChooseTag) findAncestorWithClass( ChooseTag.class ); if ( tag == null ) { throw new JellyException( "This tag must be enclosed inside a <choose> tag" ); } if ( ! tag.isBlockEvaluated() && test != null ) { | public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { value = true; invokeBody(output); } } } |
value = true; | tag.setBlockEvaluated(true); | public void doTag(XMLOutput output) throws Exception { value = false; if ( test != null ) { if ( test.evaluateAsBoolean( context ) ) { value = true; invokeBody(output); } } } |
project.setProperty("ant.file", context.getCurrentURL().toExternalForm()); | public static Project createProject(JellyContext context) { GrantProject project = new GrantProject(); project.setPropsHandler(new JellyPropsHandler(context)); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.... | |
public void doTag(final XMLOutput output) throws Exception { | public void doTag(final XMLOutput output) throws JellyTagException { | public void doTag(final XMLOutput output) throws Exception { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ... |
throw new JellyException( "Could not find a TestSuite to add this test to. This tag should be inside a <test:suite> tag" ); | throw new JellyTagException( "Could not find a TestSuite to add this test to. This tag should be inside a <test:suite> tag" ); | public void doTag(final XMLOutput output) throws Exception { String name = getName(); if ( name == null ) { name = toString(); } // #### we need to redirect the output to a TestListener // or something? TestCase testCase = new TestCase(name) { ... |
registerTag("properties", PropertiesTag.class); | public UtilTagLibrary() { registerTag("tokenize", TokenizeTag.class); } | |
boolean definedHere = answer != null || variables.containsKey(name); if (definedHere) return answer; | public Object findVariable(String name) { Object answer = variables.get(name); if ( answer == null && parent != null ) { answer = parent.findVariable(name); } // ### this is a hack - remove this when we have support for pluggable Scopes if ( answer == null ) { ... | |
if (definedHere) return value; | public Object getVariable(String name) { Object value = variables.get(name); if ( value == null && isInherit() ) { JellyContext parent = getParent(); if (parent != null) { value = parent.getVariable( name ); } } // ### thi... | |
instance.delete(); | public void removeInstance( int instanceNum ) throws IndexOutOfBoundsException { ODMGXAWrapper txw = new ODMGXAWrapper(); ImageInstance instance = null; try { instance = (ImageInstance) getInstances().get(instanceNum ); } catch ( IndexOutOfBoundsException e ) { ... | |
this.selectionTimer = new Timer(500, new ActionListener() { public void actionPerformed(final ActionEvent e) { selectDocument(document.getId()); } }); | private ListItem(final Document document) { super("DocumentListAvatar$ListItem", listItemBackground); this.document = document; this.selectionTimer = new Timer(500, new ActionListener() { public void actionPerformed(final ActionEvent e) { selectDocument(document.getId()); } }); setLayout(new GridB... | |
public void mouseEntered(final MouseEvent e) { startSelectionTimer(); } | public void mouseEntered(final MouseEvent e) { selectDocument(document.getId()); } | public void mouseEntered(final MouseEvent e) { startSelectionTimer(); } |
stopSelectionTimer(); unselect(); | unselectDocument(document.getId()); | public void mouseExited(final MouseEvent e) { stopSelectionTimer(); unselect(); } |
selectionTimer.stop(); | private void select() { selectionTimer.stop(); setBackground(listItemBackgroundSelect); repaint(); } | |
this.selectionTimer = new Timer(500, new ActionListener() { public void actionPerformed(ActionEvent e) { controller.selectDocument(currentSelection); } }); this.selectionTimer.setRepeats(false); | DocumentListAvatar(final Controller controller) { super("DocumentListAvatar", new Color(255, 255, 255, 255)); this.controller = controller; this.documentItemMap = new Hashtable<UUID, Component>(20, 0.75F); setLayout(new GridBagLayout()); } | |
controller.selectDocument(documentId); | currentSelection = documentId; selectionTimer.start(); | private void selectDocument(final UUID documentId) { Assert.assertNotNull("Cannot select null document.", documentId); // if it's the same do nothing if(this.currentSelection == documentId || documentId.equals(currentSelection)) { return; } final Collection<Component> listItems = documentItemMap.values(); for(... |
dtde.acceptDrop(DnDConstants.ACTION_COPY); c.importTableCopy((SQLTable) someData, dropLoc); dtde.dropComplete(true); return; | TablePane tp = c.importTableCopy((SQLTable) someData, dropLoc); dropLoc.x += tp.getPreferredSize().width + 5; | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... |
dtde.acceptDrop(DnDConstants.ACTION_COPY); | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... | |
dtde.dropComplete(true); return; | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... | |
c.importTableCopy(sourceTable, dropLoc); | TablePane tp = c.importTableCopy(sourceTable, dropLoc); dropLoc.x += tp.getPreferredSize().width + 5; | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... |
ufe.printStackTrace(); | logger.error(ufe); | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... |
ioe.printStackTrace(); | logger.error(ioe); | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... |
ex.printStackTrace(); | logger.error(ex); | public void drop(DropTargetDropEvent dtde) { if (tpTarget != null) { tpTarget.getDropTarget().drop(dtde); return; } Transferable t = dtde.getTransferable(); PlayPen c = (PlayPen) dtde.getDropTargetContext().getComponent(); DataFlavor importFlavor = bestImportFlavor(c, t.getTransferDataFlavors()); if... |
JOptionPane.showMessageDialog(SwingUtilities.getWindowAncestor(CompareDMPanel.this), "Unexpected architect exception in ConnectionListener" + "\n" + e, "Error", JOptionPane.ERROR_MESSAGE); | public void doStuff() throws Exception { try { ListerProgressBarUpdater progressBarUpdater = new ListerProgressBarUpdater(progressBar, this); new javax.swing.Timer(100, progressBarUpdater).start(); db.populate(); } catch (ArchitectException e) { logger.debug( "Unexpected architect ex... | |
String newValue = project.replaceProperties( (String) value ); | String newValue = ProjectHelper.replaceProperties( project, (String) value, project.getProperties() ); | public void setAttribute(String name, Object value) { // Catch the normal setAttribute, and call throw Ant's // normal property-deref routines. Project project = task.getProject(); String newValue = project.replaceProperties( (String) value ); super.... |
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